If you've actually ever used Emacs before don't use Aquamacs, or else you're going to end up reconfiguring everything all over again because the Aquamacs developers don't seem to like to stick the standards and conventions.
Random things are wonky and way out of place. Like their variation of how buffers and frames work is ridiculous.
Build the Nextstep version, Emacs.app and things will actually work the way they're supposed to without having to reconfigure everything again.
On the other hand, if you are used to Mac OS X applications and want to try Emacs, Aquamacs is a good place to start. Mapping the Command key to traditional Mac shortcuts (Cmd-C copy, Cmd-V paste, etc.) while leaving the Control key for Emacs commands and Option as Meta, works really well for me. I have used Emacs off and on over a couple decades now, but have also been using Macs for about as long, so changing Command to do something other than the Mac shortcuts when I am on a Mac would mess with my muscle memory something terrible. I find myself sometimes using Cmd-V to paste and sometimes C-y as the mood strikes, and somehow it all works.
So, executive summary: if you just want Emacs like its always been stay away from Aquamacs. If you want Emacs that makes a little more sense according to Mac OS interface guidelines, give Aquamacs a shot.
Actually, the Cocoa (aka "nextstep") build of GNU Emacs 23.1 works exactly this way by default. Option is Meta, and various typical Mac Cmd shortcuts work by default (many of the ones that Aquamacs supports). For example:
Cmd-C/X/V - copy/cut/paste
Cmd-Z - undo
Cmd-N - new frame (or "window" in Mac terminology)
Cmd-W - close frame (if not last frame)
Cmd-` - switch between frames
Cmd-H - hide application
Cmd-M - minimize frame
Cmd-, - customize
Cmd-K - kill buffer
Cmd-T - bring up Mac font chooser
Cmd-S - save
Cmd-A - select all
Cmd-O - bring up Mac file chooser
And of course you can define your own actions that use Cmd if you'd like.
I think, for new users, the way Emacs does frames/windows/buffers is worth discovering instead of what Aquamacs does by default.
Emacs.app already does mappings correctly. In fact the last time I checked it also uses the native clipboard better than Aquamacs does, kill and copy work the same, as with yank/paste work.
Random things are wonky and way out of place. Like their variation of how buffers and frames work is ridiculous.
Build the Nextstep version, Emacs.app and things will actually work the way they're supposed to without having to reconfigure everything again.